Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate Pf6N2E2_1649 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= TCDB::Q72L52 (376 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1649 Length = 384 Score = 329 bits (844), Expect = 7e-95 Identities = 182/367 (49%), Positives = 247/367 (67%), Gaps = 22/367 (5%) Query: 3 KVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYI 62 K++L++V K+ G ++D +LE GEFVVFVGPSGCGK+T LR+IAGL+ I +G++ I Sbjct: 3 KLKLDNVNKQLGGARILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICDGDLLI 62 Query: 63 GDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILK 122 R VND+ P++R + MVFQ+YALYPHM+VY+N++FGL+L + K + RV + A+IL+ Sbjct: 63 DGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKASLRERVLKTAQILQ 122 Query: 123 IEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRR 182 ++ LL RKPRELSGGQRQRVAMGRA+ REP + L DEPLSNLDA LRV+MR EIA+L R Sbjct: 123 LDKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHGR 182 Query: 183 LGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFV 242 LG T IYVTHDQVEAMTL +IVV+ G I+QV +P LY+ PA+RFVAGF+GSP MNF+ Sbjct: 183 LGSTMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYEHPASRFVAGFLGSPKMNFL 242 Query: 243 RAGVEVQGEKVYLVAPGFRIRANAVLGSALKPY------AGKEVWLGVRPEHLGLKGYTT 296 A + GE + +P +LG P+ G + LG+RPEH+ LK Sbjct: 243 PARLHSPGETSQIDSP--------LLGMTPLPFDSAHLAVGSPLTLGIRPEHMSLKA--- 291 Query: 297 IPEEENVLRGEVEV--VEPLGAETEIHV-AVNGTLLVAKVDGHAPVKPGDKVELLADTQR 353 + + G V V VE LG+ET +H+ + L+ + + +A + GD+VEL Sbjct: 292 --AQGSAGVGVVGVVGVEYLGSETYVHLESGEDEPLICRCEVNAGWRVGDRVELQLAFGS 349 Query: 354 LHAFDLE 360 +H FD + Sbjct: 350 VHLFDAD 356 Lambda K H 0.320 0.139 0.400 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 448 Number of extensions: 23 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 376 Length of database: 384 Length adjustment: 30 Effective length of query: 346 Effective length of database: 354 Effective search space: 122484 Effective search space used: 122484 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory